MapManhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_category?p_l_id=&mbCategoryId=13069 Everything regarding the MapMan software.Sun, 07 Jun 2020 09:06:27 GMT2020-06-07T09:06:27ZRE: citrus mappinghttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195967 Hi Siwar,<br /><br />I think there was a misunderstanding. <br /><br />We do have a mapping file for Citrus sinensis in our store from which is from phytozome, but it is V1.0. (This can also only be used with the older pathway diagrams).<br /><br />The only version I can see that is currently available on phytozome is V1.1 (which is the Csinensis_154 which your have used). <br />The gene id&#039;s have changed between these two versions. <br /><br />However, you can download the Csinensis_154_v1.1.protein.fa.gz from phytozome and submit it to the new Mercator4 at <br />https://plabipd.de/portal/mercator4<br /><br />The output of this can be used in MapMan together with you data and the pathway files (which start with X4.2_)<br /><br />If you have any problems/questions, let me know. <br />Regards,<br />Marie.Fri, 22 Nov 2019 15:05:26 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195967Marie Bolger2019-11-22T15:05:26ZRE: citrus mappinghttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195842 Hi Marie,<br />I converted my data to Citrus Sinensis phytozome: Csinensis_154, and I downloaded the mapping file from your web. as required, but I still can&#039;t run it on MapMan.<br />examples of genes ID from my work: <br />orange1.1g013346m<br />orange1.1g005037m<br />orange1.1g012820m<br />orange1.1g040288m<br />orange1.1g042954m<br />orange1.1g025077m<br />orange1.1g009399m<br />orange1.1g043627m<br />orange1.1g029568m<br />orange1.1g027229m<br />orange1.1g005321m<br />orange1.1g046764m<br />orange1.1g003680mTue, 19 Nov 2019 13:50:45 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195842siwar I. assili2019-11-19T13:50:45ZRE: citrus mappinghttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195653 Hello Siwar,<br /><br />We actively maintain the mapping files for only a select number of species on our download site (mainly the EnsemblPlants genomes)<br /><br />However, you can easily submit the Citrus Sinensis sequences to Mercator4 yourself and the output you obtain is the &#039;mapping file&#039;. <br /><br />https://www.plabipd.de/portal/mercator4<br /><br />If you have any problems submitting or retrieving the mapping file, please let me know. <br /><br />Regards,<br />Marie.Thu, 14 Nov 2019 10:37:17 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195653Marie Bolger2019-11-14T10:37:17Zcitrus mappinghttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195591 Hello,<br />I`m working with Citrus Sinensis sequence, reference type: locus ID (PLAZA3.0). Is there any way to upload it to the mapping file for using as a reference.<br />thanks,Thu, 14 Nov 2019 07:58:26 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195591siwar I. assili2019-11-14T07:58:26ZRE: problem to run Mapmanhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195122 i also can not run mapman and it always happened error to me!Mon, 28 Oct 2019 13:20:41 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=195122shan shan chen2019-10-28T13:20:41ZRE: problem to run Mapmanhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=168797 Dear luana,<br /><br />MapMan should not have any issues running on Java8<br /><br />Could you provide some additional details:-<br />Which version of MapMan are you running? <br />Which operating system are you using? <br /><br />In what way does it fail (during installation or while running)? <br /><br />Regards,<br />Marie.Tue, 30 May 2017 14:51:28 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=168797Marie Bolger2017-05-30T14:51:28Zproblem to run Mapmanhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=168768 I have java 8 and so I can&#039;t execute mapman.<br />And I can&#039;t find the older version of java to download.<br /><br />I need help,<br />thanksTue, 30 May 2017 14:17:51 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=168768luana tavares barbosa2017-05-30T14:17:51ZRE: Mapping fileshttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=166201 Dear Ravi,<br /><br />The mapping files should again be available to download as txt or xls files. <br /><br />Regards,<br />Marie.Tue, 09 May 2017 14:51:37 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=166201Marie Bolger2017-05-09T14:51:37ZMapping fileshttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=165813 Hello, <br />I am trying to download mapping files from the source for sorghum species (Sbicolor_79.m02). But the file formate appears to be .m02, which I could not convert to .txt formate. I remember previously, mapping files are available in .txt files. Would it be possible to add .txt file in the database. OR, is there any source where we can find mapping files in .txt formate. <br />Thanks, RaviTue, 25 Apr 2017 17:55:38 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=165813Ravi Valluru2017-04-25T17:55:38ZRE: Using ManMan for Medicago RNA-seq datahttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137116 Hi Pooja<br /><br />simplest is to use Mercator. As this look like standard Ids, if you can point me where to get the FAST files, I will also run it through Mercator and put it online.<br /><br />Best Wishes<br />BjörnWed, 28 Sep 2016 18:01:08 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137116Björn Usadel2016-09-28T18:01:08ZRE: New version of potato mapping file?http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137113 Hi,<br /><br />sorry I haven&#039;t seen this format yet. But if you have a multi-fast file, you can use Mercator (see link above) to easily create yourself a tailored Mapping File. It shouldn&#039;t take more than 1h or so, especially if you can submit protein translations.<br /><br />Best Wishes<br />BjörnWed, 28 Sep 2016 17:58:33 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137113Björn Usadel2016-09-28T17:58:33ZRE: Mercurator for Local Installhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137109 Dear Ayan<br /><br />sorry currently we don&#039;t offer this possibility, as it requires quite some work to get all the tools running on a cluster.<br />Why do you need this? Maybe there is another way we can help.<br /><br />Best Wishes<br />BjörnWed, 28 Sep 2016 17:55:46 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137109Björn Usadel2016-09-28T17:55:46ZMercurator for Local Installhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137100 Hello Administrator,<br /><br />I was wondering do your provide Mercurator copy for Local/standalone Install . As of now, I haven&#039;t found any link pointing me towards downloading a local copy. Any help regarding this would be appreciated <br /><br />Thanks,<br /><br />Ayan MalakarWed, 28 Sep 2016 15:50:57 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=137100Ayan Malakar2016-09-28T15:50:57ZNew version of potato mapping file?http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=123065 Hi, <br />I am stuck at the last step of RNAseq analysis. Here is the situation...<br /><br />I had 3 tissue types and two genotypes (wild type mutant) that were used for generating reads. I did RNAseq analysis and generated excel file with differential expressed genes.<br /><br />Problem: Now I want to visualize these genes in Mapman and mapman has mapping files which do not match with the locus ID of my data file. The format of my locus ID is something like ST4.03ch01:1139850-1140332 instead a geneID, such as PGSC0003DMG400032211 or transcript ID, such as PGSC0003DMT400082032.<br />So, I am not able to load my data into mapman. Could you please suggest some solution for this.<br /><br />Probably there will be new mapping file that matches with locus that I have.<br /><br />ThanksThu, 06 Aug 2015 18:30:53 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=123065Sukhwinder Singh Aulakh2015-08-06T18:30:53ZUsing ManMan for Medicago RNA-seq datahttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=116030 Could anybody help me to find MapMan IDs for all Medicago genes. <br /><br />We have Medicago RNA-seq data and expression levels for all Medicago genes with gene IDs e.g. Medtr8g015910 . But we could not map/visualize this into MapMan file until we have MapMan ID OR pacid e.g. ac235757_50.1|pacid:23040950 or IMGA|AC235757_50.1. How could we get the MapMan IDs or pacid for all Medicago genes with Medicago gene IDs. <br /><br />Any help will be greatly appreciated.Thu, 02 Apr 2015 16:47:38 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=116030Pooja P Pant2015-04-02T16:47:38Zerror message in mercatorhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=83928 Hello<br />I am not able anymore to submit jobs to mercator. Everytime I upload my file, check all boxes and click on Start, it gives me the error message &#034;internal error creating job directory&#034;. <br />it nevertheless assigns a link to the job, however, clicking on the link brings me back to the mercator start page.<br />is there a way to rewsolve this?<br />thanks in advance<br />NicoleMon, 10 Feb 2014 12:25:02 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=83928Nicole Regier2014-02-10T12:25:02ZRE: Mercator Downloadhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=68905 Hi David,<br /><br />i am sorry to tell you that there currently is no standalone download version of the mercator<br />pipeline. We are offering the mercator service for free and users can contact us directly in<br />case they want to annotate confidential data. We are happy to set up a confidentiality agreement<br />is necessary. The current version of Mercator runs on our cluster system - the outdated <br />standalone version just made use of the CPU it was installed on which can result in extremely<br />long processing times (unless it is installed on a very powerful machine).<br /><br />Please fell free to contact me directly (lohse@mpimp-golm.mpg.de) concerning the annotation of your<br />protein data file.<br /><br />best greetings,<br />MarcTue, 14 May 2013 14:23:00 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=68905Marc Lohse2013-05-14T14:23:00ZMercator Downloadhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=68896 I&#039;ve tried to download a standalone version of Mercator, since the protein fasta file I would like to run exceeds the allowed size.<br />I went to the following link:<br />http://mapman.gabipd.org/web/guest/mercator-download<br /><br />the link is broken / &#034;NOT FOUND&#034;<br /><br /><span style="font-size: 48px"><span style="font-size: 12px"><strong>Is Mercator still available for download??? </strong><br /></span></span>Please update the link on the website, or post the proper link in the Forum!<br /><br />Thank you for your work and effort!<br /><br />Best regards,<br />DavidTue, 14 May 2013 13:39:31 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=68896David Lyon2013-05-14T13:39:31ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41503 Hi Rafael,<br /><br />looking back at it, I would guess it&#039;s a problem if you use the java virtual machine which comes with the installer or to use the java virtual machine which comes with the operating system. Probably the one which came with the installer did not resolve the needed system libraries on your linujx installation.<br /><br />Have a nive day<br /> AxelWed, 21 Dec 2011 15:41:34 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41503Axel Nagel2011-12-21T15:41:34ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41487 Hi Axel,<br /><br />I don&#039;t know what was exactly the problem when I tried to install MapMan with a previous version, MapManInst-3.5.0. Perhaps (probably?) I was doing something wrong... The fact is that trying with this last version MapManInst-3.5.1R2 the installation was OK.<br /><br />Thank you for your attention!<br /><br />Best greetings,<br /><br />RafaWed, 21 Dec 2011 08:57:43 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41487Rafael Torres2011-12-21T08:57:43ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41464 Hi Rafael,<br /><br />thanks for your answer.<br />I&#039;m very sorry that I overlooked your previous message. <br />Or did we resolve that by personal communication?! <br /><br />Thanks <br /><br /> AxelTue, 20 Dec 2011 18:32:55 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41464Axel Nagel2011-12-20T18:32:55ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41459 Hello, <br /><br />Only to say that with the version MapManInst-3.5.1R2.bin I have had no problem at all. My MapMan works OK!<br /><br />Thank you!<br /><br />RafaTue, 20 Dec 2011 17:39:30 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=41459Rafael Torres2011-12-20T17:39:30ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33467 Axel, <br /><br />I&#039;ve lauched the script as you recommended and this is the output:<br /><br /><div class="lfr-code"><table><tbody><tr><td class="line-numbers"><span class="number">1</span><span class="number">2</span><span class="number">3</span><span class="number">4</span><span class="number">5</span><span class="number">6</span><span class="number">7</span><span class="number">8</span><span class="number">9</span><span class="number">10</span><span class="number">11</span><span class="number">12</span><span class="number">13</span><span class="number">14</span><span class="number">15</span></td><td class="lines"><div class="line"><br /></div><div class="line">~/Software/MapMan$ sh mapman.sh </div><div class="line">system lf: com.sun.java.swing.plaf.gtk.GTKLookAndFeel</div><div class="line">Exception in thread &#034;main&#034; java.lang.NoClassDefFoundError: org/dom4j/Element</div><div class="line">&nbsp; &nbsp; at de.rzpd.mapman.ImageAnnotator.initComponents(ImageAnnotator.java:169)</div><div class="line">&nbsp; &nbsp; at de.rzpd.mapman.ImageAnnotator.&lt;init&gt;(ImageAnnotator.java:153)</div><div class="line">&nbsp; &nbsp; at de.rzpd.mapman.ImageAnnotator.main(ImageAnnotator.java:679)</div><div class="line">Caused by: java.lang.ClassNotFoundException: org.dom4j.Element</div><div class="line">&nbsp; &nbsp; at java.net.URLClassLoader$1.run(URLClassLoader.java:217)</div><div class="line">&nbsp; &nbsp; at java.security.AccessController.doPrivileged(Native Method)</div><div class="line">&nbsp; &nbsp; at java.net.URLClassLoader.findClass(URLClassLoader.java:205)</div><div class="line">&nbsp; &nbsp; at java.lang.ClassLoader.loadClass(ClassLoader.java:321)</div><div class="line">&nbsp; &nbsp; at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)</div><div class="line">&nbsp; &nbsp; at java.lang.ClassLoader.loadClass(ClassLoader.java:266)</div><div class="line">&nbsp; &nbsp; ... 3 more</div></td></tr></tbody></table></div><br /><br />and MapMan do not start...<br /><br />Am I doing something wrong?<br /><br />RafaelFri, 03 Jun 2011 15:37:08 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33467Rafael Torres2011-06-03T15:37:08ZRE: Problems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33464 Actually, I &#039; don&#039;t know the source of the problem.<br /><br />If you are familiar with starting applications by shell scripts and you have java installed you might just start the MapMan application manually.<br /><br />Create a small shell script within the MapMan application directory: <br /><br />mapman.sh<br /><br /> <div class="lfr-code"><table><tbody><tr><td class="line-numbers"><span class="number">1</span><span class="number">2</span><span class="number">3</span><span class="number">4</span></td><td class="lines"><div class="line">java -Xmx512m -cp lib/batik-awt-util.jar:lib/batik-ext.jar:lib/batik-svg-dom.jar:lib/batik-xml.jar:lib/freehep-graphics2d.jar:lib/freehep-graphicsio-pdf.jar:lib/js.jar:lib/xerces_2_5_0.jar:lib/batik-bridge.jar:lib/batik-gui-util.jar:lib/</div><div class="line">batik-svggen.jar:lib/commons-codec.jar:lib/freehep-graphicsio-emf.jar:lib/freehep-graphicsio-ps.jar:lib/junit.jar:lib/xml-apis.jar:lib/batik-css.jar:lib/batik-gvt.jar:lib/batik-swing.jar:lib/commons-httpclient.jar:lib/freehep-graphicsio-</div><div class="line">gif.jar:lib/freehep-graphicsio-svg.jar:lib/jxl.jar:lib/YAMB.jar:lib/batik-dom.jar:lib/batik-parser.jar:lib/batik-transcoder.jar:lib/dom4j-1.5.2.jar:lib/freehep-graphicsio.jar:lib/hsqldb.jar:lib/pdf-transcoder.jar:lib/batik-extension.jar:</div><div class="line">lib/batik-script.jar:lib/batik-util.jar:lib/freehep-base.jar:lib/freehep-graphicsio-java.jar:lib/ImageAnnotator.jar:lib/poi.jar de.rzpd.mapman.ImageAnnotator</div></td></tr></tbody></table></div><br /><br />and then start <br /><br />sh mapman.sh<br /><br />Hope that helps, otherwise I have to look into it in more detail<br /><br /> AxelFri, 03 Jun 2011 13:16:44 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33464Axel Nagel2011-06-03T13:16:44ZProblems installing MapMan in Ubuntu 11.04 (64 bit)http://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33456 Hello!<br /><br />I tried to install MapMan 3.5.0 for Linux (MapManInst-3.5.0.bin) in my Ubuntu 11.04 (64 bit) but it told to me that an error occurred during the installation (I cannot find the log...) <br />In spite of that, the files and folders seems to be installed.<br />When I lauch MapMan a message appears: &#034;String: /lib/libc.so.6 no such file&#034; and the program aborts.<br />I can see that in my 64bit machine that file is not in the &#034;/lib&#034; folder but in the folders &#034;/lib/lib32&#034; and &#034;/lib/lib64/x86_64-linux-gnu&#034; folders.<br /><br />Could you help me and tell me what is wrong or what can I do?<br /><br />Thank you in advance,<br />RafaFri, 03 Jun 2011 12:32:37 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=33456Rafael Torres2011-06-03T12:32:37ZRE: MapMan installationhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=26801 Hi <br />MapMan tries to preserve previuos settings and installaed userfiles.<br />you can try in MapMan<br />File-&gt;Preferences-&gt;Reinstall<br /><br />I hope this works,<br /><br />Best Wishes,<br />BjörnWed, 13 Oct 2010 13:21:17 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=26801Björn Usadel2010-10-13T13:21:17ZMapMan installationhttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=26793 I have got some problems during the second part of the installation of MapMan. When I was asked to choice a folder (where were put in the folders experiments, mappings and pathways), I infortunately chose a wrong one. Then I tried to change the folder without any success. I de-installed completely Mapman and re-installed it, but in this case, I wasn&#039;t asked anymore about the choice of the folder. What can I do ?Wed, 13 Oct 2010 12:38:57 GMThttp://mapman.gabipd.org/ca_ES/c/message_boards/find_message?p_l_id=&messageId=26793Virginie Bourion2010-10-13T12:38:57Z